6J4Y

RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.

Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I.

(2019) Science 363: 744-747

  • DOI: 10.1126/science.aav8912
  • Primary Citation of Related Structures:  
    6IR9, 6J4W, 6J4X, 6J4Y, 6J4Z, 6J50, 6J51

  • PubMed Abstract: 

    • RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional factors in vivo. We demonstrate that the transcription elongation factors Elf1 and Spt4/5 cooperatively lower the barriers and increase the RNAPII processivity in the nucleosome ...

    RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional factors in vivo. We demonstrate that the transcription elongation factors Elf1 and Spt4/5 cooperatively lower the barriers and increase the RNAPII processivity in the nucleosome. The cryo-electron microscopy structures of the nucleosome-transcribing RNAPII elongation complexes (ECs) reveal that Elf1 and Spt4/5 reshape the EC downstream edge and intervene between RNAPII and the nucleosome. They facilitate RNAPII progression through superhelical location SHL(-1) by adjusting the nucleosome in favor of the forward progression. They suppress pausing at SHL(-5) by preventing the stable RNAPII-nucleosome interaction. Thus, the EC overcomes the nucleosomal barriers while providing a platform for various chromatin functions.

    Organizational Affiliation: 

    RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. shunichi.sekine@riken.jp kurumizaka@iam.u-tokyo.ac.jp.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunitA1,743Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_0568
EC: 2.7.7.6
UniProt
Find proteins for C4R4Y0 (Komagataella phaffii (strain GS115 / ATCC 20864))
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UniProt GroupC4R4Y0
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaB1,227Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-1_0125
EC: 2.7.7.6
UniProt
Find proteins for C4QZQ7 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II third largest subunit B44, part of central coreC304Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr4_0344
UniProt
Find proteins for C4R7L2 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit B32D186Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-2_0104
UniProt
Find proteins for C4R2U9 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase subunit ABC27, common to RNA polymerases I, II, and IIIE214Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_0157
UniProt
Find proteins for C4R3P8 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and IIIF155Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-2_0434
UniProt
Find proteins for C4R1V1 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunitG171Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr4_0906
UniProt
Find proteins for C4R9A1 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3H145Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-2_0309
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunitI115Komagataella phaffii CBS 7435Mutation(s): 0 
Gene Names: RPB9, PP7435_Chr1-1144
UniProt
Find proteins for F2QPE6 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and IIIJ72Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-1_0223
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit B12.5K118Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_0244
UniProt
Find proteins for C4R3Z5 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase subunit ABC10-alphaL72Komagataella phaffii CBS 7435Mutation(s): 0 
Gene Names: RPC10, PP7435_Chr1-0476
UniProt
Find proteins for F2QMI1 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor 1 homologP [auth M]113Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_c121_0006
UniProt
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor SPT4Q [auth V]108Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-1_0350
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Protein that forms a complex with Spt4pR [auth W]911Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_1136
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.3S [auth a],
W [auth e]		139Homo sapiensMutation(s): 0 
Gene Names: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B, H3-3A, H3-3B
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4T [auth b],
X [auth f]		106Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/EU [auth c],
Y [auth g]		133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA, H2AC4, H2AC8
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JV [auth d],
Z [auth h]		129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJ, H2BFR, H2BC11
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Entity ID: 13
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3')M [auth P]16synthetic construct
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Entity ID: 14
MoleculeChainsLengthOrganismImage
DNA (198-MER)N [auth T]198synthetic construct
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Entity ID: 15
MoleculeChainsLengthOrganismImage
DNA (198-MER)O [auth N]198synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0-beta2

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP25116002
Japan Society for the Promotion of ScienceJapanJP15H04344
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101076
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101082
Japan Science and TechnologyJapanJPMJCR16G1

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other